Starting phenix.real_space_refine on Wed Aug 7 22:44:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp9_37713/08_2024/8wp9_37713.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp9_37713/08_2024/8wp9_37713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp9_37713/08_2024/8wp9_37713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp9_37713/08_2024/8wp9_37713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp9_37713/08_2024/8wp9_37713.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp9_37713/08_2024/8wp9_37713.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.155 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 13680 2.51 5 N 3528 2.21 5 O 4176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 21432 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "P" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "T" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "U" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "E" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "I" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "X" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "D" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "R" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "O" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "C" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "B" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "W" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "K" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "N" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "H" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "L" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "M" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "Q" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "J" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "G" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "S" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "V" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Time building chain proxies: 13.07, per 1000 atoms: 0.61 Number of scatterers: 21432 At special positions: 0 Unit cell: (132.581, 132.581, 132.581, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 4176 8.00 N 3528 7.00 C 13680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.89 Conformation dependent library (CDL) restraints added in 4.3 seconds 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5136 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 48 sheets defined 11.3% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.71 Creating SS restraints... Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA A 120 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE A 140 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 66 No H-bonds generated for 'chain 'P' and resid 64 through 66' Processing helix chain 'P' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA P 120 " --> pdb=" O GLU P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE P 140 " --> pdb=" O GLU P 137 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 66 No H-bonds generated for 'chain 'T' and resid 64 through 66' Processing helix chain 'T' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA T 120 " --> pdb=" O GLU T 117 " (cutoff:3.500A) Processing helix chain 'T' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE T 140 " --> pdb=" O GLU T 137 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 66 No H-bonds generated for 'chain 'U' and resid 64 through 66' Processing helix chain 'U' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA U 120 " --> pdb=" O GLU U 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE U 140 " --> pdb=" O GLU U 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 66 No H-bonds generated for 'chain 'E' and resid 64 through 66' Processing helix chain 'E' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA E 120 " --> pdb=" O GLU E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE E 140 " --> pdb=" O GLU E 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 66 No H-bonds generated for 'chain 'I' and resid 64 through 66' Processing helix chain 'I' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA I 120 " --> pdb=" O GLU I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE I 140 " --> pdb=" O GLU I 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 66 No H-bonds generated for 'chain 'X' and resid 64 through 66' Processing helix chain 'X' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA X 120 " --> pdb=" O GLU X 117 " (cutoff:3.500A) Processing helix chain 'X' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE X 140 " --> pdb=" O GLU X 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA D 120 " --> pdb=" O GLU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE D 140 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA F 120 " --> pdb=" O GLU F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE F 140 " --> pdb=" O GLU F 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 66 No H-bonds generated for 'chain 'R' and resid 64 through 66' Processing helix chain 'R' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA R 120 " --> pdb=" O GLU R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE R 140 " --> pdb=" O GLU R 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 66 No H-bonds generated for 'chain 'O' and resid 64 through 66' Processing helix chain 'O' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA O 120 " --> pdb=" O GLU O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE O 140 " --> pdb=" O GLU O 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA C 120 " --> pdb=" O GLU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE C 140 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA B 120 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE B 140 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 66 No H-bonds generated for 'chain 'W' and resid 64 through 66' Processing helix chain 'W' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA W 120 " --> pdb=" O GLU W 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE W 140 " --> pdb=" O GLU W 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 66 No H-bonds generated for 'chain 'K' and resid 64 through 66' Processing helix chain 'K' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA K 120 " --> pdb=" O GLU K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE K 140 " --> pdb=" O GLU K 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 66 No H-bonds generated for 'chain 'N' and resid 64 through 66' Processing helix chain 'N' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA N 120 " --> pdb=" O GLU N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE N 140 " --> pdb=" O GLU N 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA H 120 " --> pdb=" O GLU H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE H 140 " --> pdb=" O GLU H 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 66 No H-bonds generated for 'chain 'L' and resid 64 through 66' Processing helix chain 'L' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA L 120 " --> pdb=" O GLU L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE L 140 " --> pdb=" O GLU L 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 66 No H-bonds generated for 'chain 'M' and resid 64 through 66' Processing helix chain 'M' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA M 120 " --> pdb=" O GLU M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE M 140 " --> pdb=" O GLU M 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 66 No H-bonds generated for 'chain 'Q' and resid 64 through 66' Processing helix chain 'Q' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA Q 120 " --> pdb=" O GLU Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE Q 140 " --> pdb=" O GLU Q 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 66 No H-bonds generated for 'chain 'J' and resid 64 through 66' Processing helix chain 'J' and resid 116 through 120 removed outlier: 3.664A pdb=" N ALA J 120 " --> pdb=" O GLU J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE J 140 " --> pdb=" O GLU J 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA G 120 " --> pdb=" O GLU G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 140 removed outlier: 3.675A pdb=" N ILE G 140 " --> pdb=" O GLU G 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 66 No H-bonds generated for 'chain 'S' and resid 64 through 66' Processing helix chain 'S' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA S 120 " --> pdb=" O GLU S 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE S 140 " --> pdb=" O GLU S 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 66 No H-bonds generated for 'chain 'V' and resid 64 through 66' Processing helix chain 'V' and resid 116 through 120 removed outlier: 3.663A pdb=" N ALA V 120 " --> pdb=" O GLU V 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 136 through 140 removed outlier: 3.674A pdb=" N ILE V 140 " --> pdb=" O GLU V 137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AA2, first strand: chain 'E' and resid 146 through 147 removed outlier: 7.786A pdb=" N ALA A 122 " --> pdb=" O GLU E 147 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR C 96 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLU A 49 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE C 94 " --> pdb=" O GLU A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 97 removed outlier: 5.633A pdb=" N ILE A 94 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU C 49 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR A 96 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA C 122 " --> pdb=" O GLU G 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 143 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 removed outlier: 3.944A pdb=" N PHE B 124 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR D 96 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU B 49 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE D 94 " --> pdb=" O GLU B 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 36 through 40 Processing sheet with id=AA7, first strand: chain 'P' and resid 121 through 125 removed outlier: 3.554A pdb=" N TYR O 96 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU P 49 " --> pdb=" O ILE O 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE O 94 " --> pdb=" O GLU P 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 93 through 97 removed outlier: 5.601A pdb=" N ILE P 94 " --> pdb=" O GLU O 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU O 49 " --> pdb=" O ILE P 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR P 96 " --> pdb=" O ILE O 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 142 through 143 Processing sheet with id=AB1, first strand: chain 'P' and resid 146 through 147 removed outlier: 3.829A pdb=" N PHE G 124 " --> pdb=" O GLU P 147 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR H 96 " --> pdb=" O ILE G 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU G 49 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE H 94 " --> pdb=" O GLU G 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 36 through 40 Processing sheet with id=AB3, first strand: chain 'R' and resid 93 through 97 removed outlier: 5.617A pdb=" N ILE R 94 " --> pdb=" O GLU T 49 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU T 49 " --> pdb=" O ILE R 94 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR R 96 " --> pdb=" O ILE T 47 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA T 122 " --> pdb=" O GLU K 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 93 through 97 removed outlier: 5.526A pdb=" N ILE T 94 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU R 49 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR T 96 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 142 through 143 Processing sheet with id=AB6, first strand: chain 'T' and resid 146 through 147 removed outlier: 4.072A pdb=" N PHE X 124 " --> pdb=" O GLU T 147 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR W 96 " --> pdb=" O ILE X 47 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLU X 49 " --> pdb=" O ILE W 94 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ILE W 94 " --> pdb=" O GLU X 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 36 through 40 Processing sheet with id=AB8, first strand: chain 'F' and resid 93 through 97 removed outlier: 5.601A pdb=" N ILE F 94 " --> pdb=" O GLU U 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU U 49 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR F 96 " --> pdb=" O ILE U 47 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA U 122 " --> pdb=" O GLU V 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 93 through 97 removed outlier: 5.601A pdb=" N ILE U 94 " --> pdb=" O GLU F 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU F 49 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR U 96 " --> pdb=" O ILE F 47 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ALA F 122 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 142 through 143 Processing sheet with id=AC2, first strand: chain 'U' and resid 146 through 147 removed outlier: 3.712A pdb=" N PHE Q 124 " --> pdb=" O GLU U 147 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR S 96 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU Q 49 " --> pdb=" O ILE S 94 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE S 94 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 36 through 40 Processing sheet with id=AC4, first strand: chain 'F' and resid 146 through 147 removed outlier: 7.830A pdb=" N ALA E 122 " --> pdb=" O GLU F 147 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR N 96 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU E 49 " --> pdb=" O ILE N 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE N 94 " --> pdb=" O GLU E 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 93 through 97 removed outlier: 5.601A pdb=" N ILE E 94 " --> pdb=" O GLU N 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU N 49 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR E 96 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 36 through 40 Processing sheet with id=AC7, first strand: chain 'I' and resid 121 through 125 removed outlier: 3.554A pdb=" N TYR K 96 " --> pdb=" O ILE I 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU I 49 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE K 94 " --> pdb=" O GLU I 49 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 93 through 97 removed outlier: 5.601A pdb=" N ILE I 94 " --> pdb=" O GLU K 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU K 49 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR I 96 " --> pdb=" O ILE K 47 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE K 124 " --> pdb=" O GLU O 147 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 142 through 143 Processing sheet with id=AD1, first strand: chain 'I' and resid 146 through 147 removed outlier: 3.760A pdb=" N PHE J 124 " --> pdb=" O GLU I 147 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR L 96 " --> pdb=" O ILE J 47 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU J 49 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE L 94 " --> pdb=" O GLU J 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'X' and resid 93 through 97 removed outlier: 5.567A pdb=" N ILE X 94 " --> pdb=" O GLU W 49 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU W 49 " --> pdb=" O ILE X 94 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR X 96 " --> pdb=" O ILE W 47 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ALA W 122 " --> pdb=" O GLU H 147 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 142 through 143 Processing sheet with id=AD4, first strand: chain 'D' and resid 36 through 40 Processing sheet with id=AD5, first strand: chain 'B' and resid 93 through 97 removed outlier: 5.750A pdb=" N ILE B 94 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLU D 49 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B 96 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ALA D 122 " --> pdb=" O GLU S 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 142 through 143 Processing sheet with id=AD7, first strand: chain 'F' and resid 36 through 40 Processing sheet with id=AD8, first strand: chain 'R' and resid 36 through 40 Processing sheet with id=AD9, first strand: chain 'R' and resid 142 through 143 Processing sheet with id=AE1, first strand: chain 'R' and resid 146 through 147 removed outlier: 4.058A pdb=" N PHE V 124 " --> pdb=" O GLU R 147 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR M 96 " --> pdb=" O ILE V 47 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU V 49 " --> pdb=" O ILE M 94 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ILE M 94 " --> pdb=" O GLU V 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 142 through 143 Processing sheet with id=AE3, first strand: chain 'C' and resid 36 through 40 Processing sheet with id=AE4, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AE5, first strand: chain 'W' and resid 36 through 40 Processing sheet with id=AE6, first strand: chain 'W' and resid 142 through 143 Processing sheet with id=AE7, first strand: chain 'N' and resid 36 through 40 Processing sheet with id=AE8, first strand: chain 'N' and resid 142 through 143 Processing sheet with id=AE9, first strand: chain 'N' and resid 146 through 147 removed outlier: 3.723A pdb=" N PHE M 124 " --> pdb=" O GLU N 147 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR V 96 " --> pdb=" O ILE M 47 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU M 49 " --> pdb=" O ILE V 94 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE V 94 " --> pdb=" O GLU M 49 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 121 through 125 removed outlier: 3.554A pdb=" N TYR G 96 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU H 49 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE G 94 " --> pdb=" O GLU H 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 121 through 125 removed outlier: 3.635A pdb=" N TYR J 96 " --> pdb=" O ILE L 47 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU L 49 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ILE J 94 " --> pdb=" O GLU L 49 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 93 through 97 removed outlier: 5.581A pdb=" N ILE Q 94 " --> pdb=" O GLU S 49 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU S 49 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) 945 hydrogen bonds defined for protein. 2331 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.35 Time building geometry restraints manager: 9.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6907 1.34 - 1.46: 1738 1.46 - 1.57: 12979 1.57 - 1.69: 0 1.69 - 1.80: 96 Bond restraints: 21720 Sorted by residual: bond pdb=" CA ILE X 45 " pdb=" CB ILE X 45 " ideal model delta sigma weight residual 1.544 1.570 -0.026 1.42e-02 4.96e+03 3.26e+00 bond pdb=" CA ILE D 45 " pdb=" CB ILE D 45 " ideal model delta sigma weight residual 1.544 1.570 -0.026 1.42e-02 4.96e+03 3.24e+00 bond pdb=" CA ILE T 45 " pdb=" CB ILE T 45 " ideal model delta sigma weight residual 1.544 1.569 -0.025 1.42e-02 4.96e+03 3.21e+00 bond pdb=" CA ILE Q 45 " pdb=" CB ILE Q 45 " ideal model delta sigma weight residual 1.544 1.569 -0.025 1.42e-02 4.96e+03 3.18e+00 bond pdb=" CA ILE L 45 " pdb=" CB ILE L 45 " ideal model delta sigma weight residual 1.544 1.569 -0.025 1.42e-02 4.96e+03 3.17e+00 ... (remaining 21715 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.34: 721 107.34 - 114.00: 12802 114.00 - 120.67: 7801 120.67 - 127.33: 7812 127.33 - 134.00: 168 Bond angle restraints: 29304 Sorted by residual: angle pdb=" CA GLU V 101 " pdb=" CB GLU V 101 " pdb=" CG GLU V 101 " ideal model delta sigma weight residual 114.10 121.34 -7.24 2.00e+00 2.50e-01 1.31e+01 angle pdb=" CA GLU D 101 " pdb=" CB GLU D 101 " pdb=" CG GLU D 101 " ideal model delta sigma weight residual 114.10 121.33 -7.23 2.00e+00 2.50e-01 1.31e+01 angle pdb=" CA GLU T 101 " pdb=" CB GLU T 101 " pdb=" CG GLU T 101 " ideal model delta sigma weight residual 114.10 121.32 -7.22 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CA GLU X 101 " pdb=" CB GLU X 101 " pdb=" CG GLU X 101 " ideal model delta sigma weight residual 114.10 121.31 -7.21 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CA GLU J 101 " pdb=" CB GLU J 101 " pdb=" CG GLU J 101 " ideal model delta sigma weight residual 114.10 121.31 -7.21 2.00e+00 2.50e-01 1.30e+01 ... (remaining 29299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 12126 17.73 - 35.45: 1266 35.45 - 53.18: 144 53.18 - 70.91: 24 70.91 - 88.63: 48 Dihedral angle restraints: 13608 sinusoidal: 5688 harmonic: 7920 Sorted by residual: dihedral pdb=" CB GLU I 49 " pdb=" CG GLU I 49 " pdb=" CD GLU I 49 " pdb=" OE1 GLU I 49 " ideal model delta sinusoidal sigma weight residual 0.00 -81.67 81.67 1 3.00e+01 1.11e-03 9.12e+00 dihedral pdb=" CB GLU N 49 " pdb=" CG GLU N 49 " pdb=" CD GLU N 49 " pdb=" OE1 GLU N 49 " ideal model delta sinusoidal sigma weight residual 0.00 -81.67 81.67 1 3.00e+01 1.11e-03 9.12e+00 dihedral pdb=" CB GLU O 49 " pdb=" CG GLU O 49 " pdb=" CD GLU O 49 " pdb=" OE1 GLU O 49 " ideal model delta sinusoidal sigma weight residual 0.00 -81.67 81.67 1 3.00e+01 1.11e-03 9.12e+00 ... (remaining 13605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1506 0.033 - 0.066: 1096 0.066 - 0.099: 410 0.099 - 0.132: 348 0.132 - 0.166: 120 Chirality restraints: 3480 Sorted by residual: chirality pdb=" CA ILE P 35 " pdb=" N ILE P 35 " pdb=" C ILE P 35 " pdb=" CB ILE P 35 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CA ILE B 35 " pdb=" N ILE B 35 " pdb=" C ILE B 35 " pdb=" CB ILE B 35 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CA ILE G 35 " pdb=" N ILE G 35 " pdb=" C ILE G 35 " pdb=" CB ILE G 35 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 3477 not shown) Planarity restraints: 3720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU W 133 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO W 134 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO W 134 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO W 134 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 133 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO C 134 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 134 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 134 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU Q 133 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO Q 134 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO Q 134 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO Q 134 " -0.019 5.00e-02 4.00e+02 ... (remaining 3717 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 5552 2.83 - 3.35: 15205 3.35 - 3.87: 31265 3.87 - 4.38: 35621 4.38 - 4.90: 67567 Nonbonded interactions: 155210 Sorted by model distance: nonbonded pdb=" OE1 GLU D 78 " pdb=" OG1 THR D 108 " model vdw 2.315 3.040 nonbonded pdb=" OE1 GLU C 78 " pdb=" OG1 THR C 108 " model vdw 2.315 3.040 nonbonded pdb=" OE1 GLU M 78 " pdb=" OG1 THR M 108 " model vdw 2.315 3.040 nonbonded pdb=" OE1 GLU L 78 " pdb=" OG1 THR L 108 " model vdw 2.315 3.040 nonbonded pdb=" OE1 GLU R 78 " pdb=" OG1 THR R 108 " model vdw 2.315 3.040 ... (remaining 155205 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.080 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 65.760 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21720 Z= 0.350 Angle : 0.949 7.239 29304 Z= 0.532 Chirality : 0.061 0.166 3480 Planarity : 0.006 0.034 3720 Dihedral : 15.191 88.632 8472 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.00 % Allowed : 4.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.16), residues: 2712 helix: None (None), residues: 0 sheet: 3.06 (0.15), residues: 1392 loop : -1.54 (0.12), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP O 59 HIS 0.002 0.001 HIS C 53 PHE 0.005 0.001 PHE R 42 TYR 0.012 0.003 TYR M 106 ARG 0.002 0.001 ARG L 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 807 time to evaluate : 2.672 Fit side-chains revert: symmetry clash REVERT: X 147 GLU cc_start: 0.6990 (pp20) cc_final: 0.6717 (pp20) REVERT: D 98 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7273 (mt-10) REVERT: B 147 GLU cc_start: 0.5987 (pp20) cc_final: 0.5740 (pp20) outliers start: 24 outliers final: 0 residues processed: 824 average time/residue: 1.6325 time to fit residues: 1484.8859 Evaluate side-chains 475 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 475 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 206 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 239 optimal weight: 10.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 119 ASN P 36 GLN P 119 ASN T 36 GLN T 119 ASN T 126 ASN U 36 GLN U 119 ASN E 36 GLN I 36 GLN I 119 ASN X 53 HIS F 53 HIS R 36 GLN O 53 HIS C 36 GLN B 53 HIS W 36 GLN K 36 GLN N 36 GLN N 119 ASN H 36 GLN L 36 GLN L 145 ASN M 36 GLN M 119 ASN Q 53 HIS Q 119 ASN J 36 GLN J 119 ASN G 53 HIS S 36 GLN V 36 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21720 Z= 0.280 Angle : 0.722 8.905 29304 Z= 0.369 Chirality : 0.055 0.152 3480 Planarity : 0.005 0.033 3720 Dihedral : 4.736 16.071 2880 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.67 % Allowed : 20.38 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.09 (0.15), residues: 1392 loop : -0.93 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Q 59 HIS 0.007 0.001 HIS O 53 PHE 0.011 0.001 PHE X 124 TYR 0.008 0.002 TYR R 96 ARG 0.003 0.001 ARG P 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 647 time to evaluate : 2.757 Fit side-chains REVERT: A 93 ARG cc_start: 0.8277 (pmt170) cc_final: 0.7937 (pmt170) REVERT: A 102 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: E 49 GLU cc_start: 0.7802 (tt0) cc_final: 0.7563 (tt0) REVERT: E 78 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7770 (tm-30) REVERT: E 102 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6924 (mt-10) REVERT: E 104 GLU cc_start: 0.7336 (tp30) cc_final: 0.7092 (mm-30) REVERT: I 49 GLU cc_start: 0.7776 (tt0) cc_final: 0.7572 (tt0) REVERT: I 103 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7254 (mt-10) REVERT: X 92 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: D 36 GLN cc_start: 0.8033 (mt0) cc_final: 0.7816 (tt0) REVERT: D 78 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: F 78 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: F 118 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6810 (mp0) REVERT: R 78 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: R 118 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: O 78 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: O 118 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: C 78 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: C 118 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6825 (mp0) REVERT: K 49 GLU cc_start: 0.7812 (tt0) cc_final: 0.7579 (tt0) REVERT: K 78 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: K 102 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6924 (mt-10) REVERT: K 104 GLU cc_start: 0.7335 (tp30) cc_final: 0.7085 (mm-30) REVERT: N 103 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: L 78 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7648 (tm-30) REVERT: L 104 GLU cc_start: 0.7350 (tp30) cc_final: 0.7108 (mm-30) REVERT: M 49 GLU cc_start: 0.7809 (tt0) cc_final: 0.7594 (tt0) REVERT: Q 92 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7669 (mt-10) REVERT: V 78 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7831 (tm-30) outliers start: 112 outliers final: 16 residues processed: 717 average time/residue: 1.6920 time to fit residues: 1334.4207 Evaluate side-chains 575 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 539 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain N residue 103 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain Q residue 92 GLU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 78 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 199 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 240 optimal weight: 7.9990 chunk 259 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 53 HIS X 119 ASN D 119 ASN F 53 HIS O 53 HIS B 53 HIS B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 53 HIS Q 119 ASN J 119 ASN G 53 HIS G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.7505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 21720 Z= 0.270 Angle : 0.670 8.866 29304 Z= 0.339 Chirality : 0.054 0.148 3480 Planarity : 0.004 0.030 3720 Dihedral : 4.459 14.862 2880 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 4.21 % Allowed : 21.21 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.11 (0.15), residues: 1392 loop : -0.71 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 59 HIS 0.006 0.001 HIS G 53 PHE 0.006 0.001 PHE M 124 TYR 0.011 0.002 TYR N 106 ARG 0.002 0.000 ARG K 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 568 time to evaluate : 2.753 Fit side-chains REVERT: A 102 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: P 103 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7406 (mm-30) REVERT: U 103 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7401 (mm-30) REVERT: E 102 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: E 104 GLU cc_start: 0.7407 (tp30) cc_final: 0.7101 (mm-30) REVERT: X 92 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7720 (mt-10) REVERT: D 78 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: D 91 SER cc_start: 0.5854 (OUTLIER) cc_final: 0.5559 (t) REVERT: F 78 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: F 118 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: R 78 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: R 118 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: O 78 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: O 118 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: C 78 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: C 118 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: W 78 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: K 102 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7105 (mt-10) REVERT: K 104 GLU cc_start: 0.7401 (tp30) cc_final: 0.7094 (mm-30) REVERT: N 49 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: H 78 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: H 91 SER cc_start: 0.5934 (OUTLIER) cc_final: 0.5703 (t) REVERT: L 78 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: L 102 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: L 104 GLU cc_start: 0.7392 (tp30) cc_final: 0.7167 (mm-30) REVERT: M 110 LYS cc_start: 0.8846 (tttm) cc_final: 0.8599 (tttm) REVERT: Q 92 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7635 (mt-10) REVERT: J 49 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: J 78 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: J 102 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7310 (mt-10) REVERT: J 110 LYS cc_start: 0.8838 (tttm) cc_final: 0.8588 (tttm) REVERT: S 78 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7730 (tm-30) REVERT: S 91 SER cc_start: 0.5883 (OUTLIER) cc_final: 0.5663 (t) REVERT: V 78 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7841 (tm-30) outliers start: 101 outliers final: 37 residues processed: 636 average time/residue: 1.7525 time to fit residues: 1239.9085 Evaluate side-chains 615 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 549 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 121 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain N residue 49 GLU Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain Q residue 92 GLU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain S residue 46 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 91 SER Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 102 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.4980 chunk 180 optimal weight: 10.0000 chunk 124 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 255 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.7647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 21720 Z= 0.271 Angle : 0.658 8.711 29304 Z= 0.332 Chirality : 0.053 0.148 3480 Planarity : 0.004 0.031 3720 Dihedral : 4.387 14.893 2880 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 5.12 % Allowed : 20.88 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.12 (0.15), residues: 1392 loop : -0.63 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 59 HIS 0.002 0.001 HIS T 53 PHE 0.007 0.001 PHE M 124 TYR 0.009 0.002 TYR L 106 ARG 0.002 0.000 ARG E 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 575 time to evaluate : 2.816 Fit side-chains REVERT: A 78 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: A 103 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7383 (mm-30) REVERT: P 78 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: T 78 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7711 (tm-30) REVERT: T 103 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7445 (mm-30) REVERT: U 78 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: E 78 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: E 102 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7224 (mt-10) REVERT: E 104 GLU cc_start: 0.7401 (tp30) cc_final: 0.7108 (mm-30) REVERT: I 49 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7487 (tt0) REVERT: X 92 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7698 (mt-10) REVERT: D 78 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: D 91 SER cc_start: 0.5786 (OUTLIER) cc_final: 0.5545 (t) REVERT: F 78 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: F 118 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: R 49 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: R 78 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: R 118 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: O 78 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: O 118 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: C 78 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: C 118 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6848 (mp0) REVERT: W 78 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7723 (tm-30) REVERT: W 91 SER cc_start: 0.5733 (OUTLIER) cc_final: 0.5491 (t) REVERT: K 78 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: K 102 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7222 (mt-10) REVERT: K 104 GLU cc_start: 0.7396 (tp30) cc_final: 0.7112 (mm-30) REVERT: H 78 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: H 91 SER cc_start: 0.5823 (OUTLIER) cc_final: 0.5585 (t) REVERT: L 78 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: L 102 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: M 49 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: Q 49 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7482 (tt0) REVERT: J 78 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7718 (tm-30) REVERT: J 110 LYS cc_start: 0.8859 (tttm) cc_final: 0.8591 (tttm) REVERT: S 78 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: V 78 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7825 (tm-30) outliers start: 123 outliers final: 49 residues processed: 665 average time/residue: 1.6083 time to fit residues: 1184.6303 Evaluate side-chains 638 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 555 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 103 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 145 ASN Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain S residue 46 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain V residue 121 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 3 optimal weight: 0.0050 chunk 190 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.7665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 21720 Z= 0.283 Angle : 0.663 8.854 29304 Z= 0.334 Chirality : 0.054 0.147 3480 Planarity : 0.004 0.033 3720 Dihedral : 4.377 14.470 2880 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.38 % Allowed : 22.79 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.10 (0.15), residues: 1392 loop : -0.59 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Q 59 HIS 0.002 0.001 HIS T 53 PHE 0.007 0.001 PHE M 124 TYR 0.010 0.002 TYR K 106 ARG 0.002 0.000 ARG K 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 568 time to evaluate : 2.587 Fit side-chains REVERT: A 37 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8751 (mm) REVERT: A 78 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: P 78 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7724 (tm-30) REVERT: P 103 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7490 (mm-30) REVERT: T 78 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: T 103 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7468 (mm-30) REVERT: U 78 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7723 (tm-30) REVERT: U 103 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7486 (mm-30) REVERT: E 78 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: E 102 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7284 (mt-10) REVERT: E 104 GLU cc_start: 0.7379 (tp30) cc_final: 0.7171 (mm-30) REVERT: I 102 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: X 92 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: D 78 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: D 91 SER cc_start: 0.5810 (OUTLIER) cc_final: 0.5600 (t) REVERT: F 78 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7649 (tm-30) REVERT: F 118 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: R 78 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: R 118 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: O 78 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7661 (tm-30) REVERT: O 118 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: C 78 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7656 (tm-30) REVERT: C 118 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: W 78 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: W 91 SER cc_start: 0.5721 (OUTLIER) cc_final: 0.5488 (t) REVERT: K 78 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: K 102 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7276 (mt-10) REVERT: K 104 GLU cc_start: 0.7396 (tp30) cc_final: 0.7175 (mm-30) REVERT: N 102 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: H 78 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: H 91 SER cc_start: 0.5804 (OUTLIER) cc_final: 0.5582 (t) REVERT: L 78 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: M 102 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: J 78 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: J 102 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7427 (mt-10) REVERT: S 78 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: V 78 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7803 (tm-30) outliers start: 105 outliers final: 52 residues processed: 651 average time/residue: 1.5990 time to fit residues: 1151.6771 Evaluate side-chains 646 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 559 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 103 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 145 ASN Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain S residue 46 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain V residue 121 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 255 optimal weight: 0.7980 chunk 212 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.7715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 21720 Z= 0.242 Angle : 0.629 8.680 29304 Z= 0.316 Chirality : 0.053 0.147 3480 Planarity : 0.004 0.030 3720 Dihedral : 4.247 13.981 2880 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 4.29 % Allowed : 23.38 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.09 (0.15), residues: 1392 loop : -0.51 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP X 59 HIS 0.002 0.001 HIS T 53 PHE 0.006 0.001 PHE M 124 TYR 0.008 0.002 TYR V 106 ARG 0.002 0.000 ARG K 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 564 time to evaluate : 2.792 Fit side-chains REVERT: A 37 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8726 (mm) REVERT: A 78 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: P 78 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: P 103 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7457 (mm-30) REVERT: T 78 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: T 103 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: U 78 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: U 103 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7451 (mm-30) REVERT: E 78 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: E 102 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: E 104 GLU cc_start: 0.7349 (tp30) cc_final: 0.7134 (mm-30) REVERT: I 49 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: I 102 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: X 92 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: F 78 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: F 118 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: R 49 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7480 (tt0) REVERT: R 78 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: R 118 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: O 78 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: O 118 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: C 78 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: C 118 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: W 78 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: W 91 SER cc_start: 0.5707 (OUTLIER) cc_final: 0.5484 (t) REVERT: K 78 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: K 102 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7277 (mt-10) REVERT: K 104 GLU cc_start: 0.7375 (tp30) cc_final: 0.7167 (mm-30) REVERT: K 110 LYS cc_start: 0.8841 (tttm) cc_final: 0.8570 (tttm) REVERT: N 102 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7451 (mt-10) REVERT: H 78 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7730 (tm-30) REVERT: H 91 SER cc_start: 0.5817 (OUTLIER) cc_final: 0.5612 (t) REVERT: H 102 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7385 (mt-10) REVERT: M 49 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: M 102 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7462 (mt-10) REVERT: Q 49 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: J 78 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: J 102 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: S 78 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7728 (tm-30) REVERT: V 78 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7818 (tm-30) outliers start: 103 outliers final: 50 residues processed: 643 average time/residue: 1.3760 time to fit residues: 980.5695 Evaluate side-chains 644 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 557 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 103 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 121 SER Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 145 ASN Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain S residue 46 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain V residue 121 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 254 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.7710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 21720 Z= 0.368 Angle : 0.723 9.550 29304 Z= 0.365 Chirality : 0.055 0.149 3480 Planarity : 0.004 0.042 3720 Dihedral : 4.573 14.812 2880 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.67 % Allowed : 23.46 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.02 (0.15), residues: 1392 loop : -0.59 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 59 HIS 0.002 0.001 HIS T 53 PHE 0.007 0.001 PHE M 124 TYR 0.008 0.002 TYR A 106 ARG 0.002 0.001 ARG H 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 564 time to evaluate : 2.718 Fit side-chains REVERT: A 37 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8755 (mm) REVERT: A 78 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: P 78 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: P 103 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7546 (mm-30) REVERT: T 78 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: T 103 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7506 (mm-30) REVERT: U 78 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: U 103 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7535 (mm-30) REVERT: E 78 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: E 102 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: E 104 GLU cc_start: 0.7376 (tp30) cc_final: 0.7154 (mm-30) REVERT: I 102 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: X 92 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7411 (mt-10) REVERT: D 78 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: F 78 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: F 118 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6848 (mp0) REVERT: R 49 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: R 78 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: R 118 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: O 78 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: O 118 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: C 78 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: C 118 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: B 49 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.6834 (tm-30) REVERT: W 78 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: W 91 SER cc_start: 0.5729 (OUTLIER) cc_final: 0.5516 (t) REVERT: W 102 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: K 78 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: K 104 GLU cc_start: 0.7344 (tp30) cc_final: 0.7141 (mm-30) REVERT: N 102 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: H 78 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: H 102 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: L 78 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: M 49 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: M 102 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: Q 49 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: J 78 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: J 102 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7448 (mt-10) REVERT: S 78 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: V 78 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7847 (tm-30) outliers start: 112 outliers final: 50 residues processed: 644 average time/residue: 1.5411 time to fit residues: 1102.7462 Evaluate side-chains 646 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 558 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 103 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 40 LYS Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain W residue 40 LYS Chi-restraints excluded: chain W residue 46 SER Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain Q residue 49 GLU Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain S residue 40 LYS Chi-restraints excluded: chain S residue 46 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 151 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 173 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 231 optimal weight: 0.0270 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.7787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21720 Z= 0.132 Angle : 0.528 8.088 29304 Z= 0.265 Chirality : 0.051 0.143 3480 Planarity : 0.003 0.023 3720 Dihedral : 3.764 12.723 2880 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.25 % Allowed : 25.50 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.18), residues: 2712 helix: None (None), residues: 0 sheet: 3.13 (0.15), residues: 1392 loop : -0.23 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 59 HIS 0.002 0.000 HIS T 53 PHE 0.004 0.001 PHE M 124 TYR 0.008 0.001 TYR F 106 ARG 0.001 0.000 ARG R 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 569 time to evaluate : 2.702 Fit side-chains REVERT: A 78 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: P 78 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7784 (tm-30) REVERT: P 103 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7415 (mm-30) REVERT: T 78 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: T 103 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7406 (mm-30) REVERT: U 78 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: U 103 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7410 (mm-30) REVERT: E 78 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: E 104 GLU cc_start: 0.7351 (tp30) cc_final: 0.7139 (mm-30) REVERT: E 110 LYS cc_start: 0.8858 (tttm) cc_final: 0.8616 (tttm) REVERT: I 102 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7451 (mt-10) REVERT: D 78 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: F 118 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: R 118 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: O 118 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6769 (mp0) REVERT: C 118 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: W 78 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7768 (tm-30) REVERT: K 78 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: K 110 LYS cc_start: 0.8865 (ttpt) cc_final: 0.8468 (tttm) REVERT: N 102 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: H 78 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: H 102 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7314 (mt-10) REVERT: L 78 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: L 110 LYS cc_start: 0.8866 (tttm) cc_final: 0.8620 (tttm) REVERT: M 102 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: J 102 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7416 (mt-10) REVERT: S 78 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: V 110 LYS cc_start: 0.8863 (tttm) cc_final: 0.8616 (tttm) outliers start: 78 outliers final: 43 residues processed: 630 average time/residue: 1.5265 time to fit residues: 1068.8557 Evaluate side-chains 620 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 554 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 103 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 145 ASN Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 145 ASN Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 145 ASN Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 145 ASN Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 145 ASN Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain V residue 145 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 1.9990 chunk 222 optimal weight: 5.9990 chunk 237 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.7704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 21720 Z= 0.230 Angle : 0.618 8.701 29304 Z= 0.309 Chirality : 0.053 0.146 3480 Planarity : 0.004 0.030 3720 Dihedral : 4.072 13.224 2880 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.12 % Allowed : 26.12 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.10 (0.15), residues: 1392 loop : -0.33 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 59 HIS 0.002 0.001 HIS T 53 PHE 0.005 0.001 PHE M 124 TYR 0.010 0.002 TYR F 106 ARG 0.001 0.000 ARG K 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 570 time to evaluate : 2.724 Fit side-chains REVERT: A 78 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: P 78 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: P 103 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7451 (mm-30) REVERT: T 78 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: T 103 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7435 (mm-30) REVERT: U 78 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: U 103 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7444 (mm-30) REVERT: E 78 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: E 102 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7234 (mt-10) REVERT: E 104 GLU cc_start: 0.7324 (tp30) cc_final: 0.7095 (mm-30) REVERT: E 110 LYS cc_start: 0.8861 (tttm) cc_final: 0.8609 (tttm) REVERT: I 102 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7479 (mt-10) REVERT: D 78 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7688 (tm-30) REVERT: F 78 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: F 118 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: R 78 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: R 118 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: O 78 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7722 (tm-30) REVERT: O 118 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: C 78 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7723 (tm-30) REVERT: C 118 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: W 78 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: W 102 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: K 78 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: N 102 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7474 (mt-10) REVERT: H 78 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7728 (tm-30) REVERT: H 102 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7371 (mt-10) REVERT: L 78 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: L 110 LYS cc_start: 0.8865 (tttm) cc_final: 0.8613 (tttm) REVERT: M 102 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: M 142 LYS cc_start: 0.8162 (mptt) cc_final: 0.7846 (mptt) REVERT: J 78 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: J 102 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: S 78 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: S 102 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: V 110 LYS cc_start: 0.8871 (tttm) cc_final: 0.8620 (tttm) outliers start: 75 outliers final: 32 residues processed: 627 average time/residue: 1.6084 time to fit residues: 1115.3582 Evaluate side-chains 628 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 565 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 103 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 263 optimal weight: 0.9990 chunk 242 optimal weight: 0.9990 chunk 209 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.7801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21720 Z= 0.184 Angle : 0.587 8.469 29304 Z= 0.293 Chirality : 0.052 0.147 3480 Planarity : 0.003 0.025 3720 Dihedral : 3.928 12.973 2880 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.62 % Allowed : 26.92 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.17), residues: 2712 helix: None (None), residues: 0 sheet: 3.09 (0.15), residues: 1392 loop : -0.25 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 59 HIS 0.002 0.000 HIS T 53 PHE 0.005 0.001 PHE M 124 TYR 0.005 0.001 TYR G 106 ARG 0.001 0.000 ARG K 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 549 time to evaluate : 2.691 Fit side-chains REVERT: A 78 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: P 78 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7752 (tm-30) REVERT: P 103 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7416 (mm-30) REVERT: T 78 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7773 (tm-30) REVERT: T 103 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7413 (mm-30) REVERT: U 78 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: U 103 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7412 (mm-30) REVERT: E 78 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: E 104 GLU cc_start: 0.7328 (tp30) cc_final: 0.7109 (mm-30) REVERT: E 110 LYS cc_start: 0.8859 (tttm) cc_final: 0.8610 (tttm) REVERT: I 102 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7470 (mt-10) REVERT: D 78 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: F 78 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7724 (tm-30) REVERT: F 118 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: R 78 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7722 (tm-30) REVERT: R 118 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: O 78 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: O 118 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6825 (mp0) REVERT: C 78 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: C 118 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: W 78 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: K 78 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: N 102 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: H 78 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: H 102 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: L 78 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: L 110 LYS cc_start: 0.8862 (tttm) cc_final: 0.8610 (tttm) REVERT: M 102 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: J 102 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7424 (mt-10) REVERT: S 78 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7748 (tm-30) REVERT: S 102 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: V 110 LYS cc_start: 0.8867 (tttm) cc_final: 0.8615 (tttm) outliers start: 63 outliers final: 30 residues processed: 603 average time/residue: 1.6631 time to fit residues: 1116.1787 Evaluate side-chains 603 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 545 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain P residue 78 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 107 ARG Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 84 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 103 GLU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 102 GLU Chi-restraints excluded: chain U residue 103 GLU Chi-restraints excluded: chain U residue 107 ARG Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain R residue 78 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 118 GLU Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain H residue 78 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain Q residue 102 GLU Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain V residue 92 GLU Chi-restraints excluded: chain V residue 102 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 193 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 0.0870 chunk 209 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 184 optimal weight: 0.9980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN P 119 ASN T 119 ASN U 119 ASN E 119 ASN I 119 ASN X 119 ASN D 119 ASN F 119 ASN R 119 ASN O 119 ASN C 119 ASN B 119 ASN W 119 ASN K 119 ASN N 119 ASN H 119 ASN L 119 ASN M 119 ASN Q 119 ASN J 119 ASN G 119 ASN S 119 ASN V 119 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.138455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111997 restraints weight = 23408.165| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.22 r_work: 0.3147 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.7738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 21720 Z= 0.123 Angle : 0.525 7.497 29304 Z= 0.262 Chirality : 0.051 0.142 3480 Planarity : 0.003 0.023 3720 Dihedral : 3.562 12.258 2880 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.42 % Allowed : 27.33 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.18), residues: 2712 helix: None (None), residues: 0 sheet: 3.14 (0.15), residues: 1392 loop : -0.01 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP L 59 HIS 0.002 0.000 HIS T 53 PHE 0.004 0.001 PHE M 124 TYR 0.011 0.001 TYR P 106 ARG 0.001 0.000 ARG T 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15836.18 seconds wall clock time: 272 minutes 54.49 seconds (16374.49 seconds total)